HEMCO ERROR: Field has no time/date variable - cycle flag mustbe set to C in the HEMCO configuration file:BC_ACTA

[Naaimaben]

What happened? What did you expect to happen?

While running ./gcclassic i got the following error:

HEMCO: Opening /home/xx/lustre//shared/ExtData//GEOS_0.25x0.3125/GEOS_FP/2019/07/GEOSFP.20190702.I3.025x03125.nc
HEMCO: Opening /home/xx/gc_025x03125_geosfp_fullchem/OutputDir/GEOSChem.BoundaryConditions.20190701_0000z.nc4
HEMCO ERROR: Field has no time/date variable - cycle flag mustbe set to `C` in the HEMCO configuration file:BC_ACTA
HEMCO ERROR: ERROR 1
 --> LOCATION: HCOIO_READ (HCOIO_READ_STD_MOD.F90)
HEMCO ERROR: Error encountered in routine HCOIO_Read!
HEMCO ERROR: Error in HCOIO_DATAREAD called from HEMCO ReadList_Fill: BC_ACTA
 --> LOCATION: ReadList_Fill (HCO_ReadList_Mod.F90)
 --> LOCATION: ReadList_Read (HCO_ReadList_Mod.F90)
 Error in ReadList_Read called from hco_run
===============================================================================                                                                         
GEOS-Chem ERROR: Error encountered in "HCO_Run"!
 -> at HCOI_GC_Run (in module GeosCore/hco_interface_gc_mod.F90)
THIS ERROR ORIGINATED IN HEMCO!  Please check the HEMCO log file for
additional error messages!
===============================================================================                                                                         
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.                                                                         
Backtrace for this error:
#0  0x154bce47a5af in ???
#1  0x154bcefe50ad in sflush

What are the steps to reproduce the bug?

running ./gcclassic

Please attach any relevant configuration and log files.

No response

What GEOS-Chem version were you using?

14.4.2

What environment were you running GEOS-Chem on?

Other (please explain below)

What compiler and version were you using?

gcc

Will you be addressing this bug yourself?

Yes

In what configuration were you running GEOS-Chem?

GCClassic

What simulation were you running?

Full chemistry

As what resolution were you running GEOS-Chem?

0.25x0.325

What meterology fields did you use?

GEOS-FP

Additional information

No response

[yantosca]

Thanks for writing @Naaimaben. The boundary conditions are specified in the HEMCO_Config.rc file in this entry:

#==============================================================================
# --- GEOS-Chem boundary condition file ---
#==============================================================================
(((GC_BCs
* BC_  $ROOT/SAMPLE_BCs/GC_14.3.0/fullchem/GEOSChem.BoundaryConditions.$YYYY$MM$DD_$HH$MNz.nc4 SpeciesBC_?ADV? 1900-2100/1-12/1-31/* EFY xyz 1 * - 1 1
)))GC_BCs

We provide some sample BC data for testing but you will need to change $ROOT/SAMPLE_BCs/GC_14.3.0/fullchem/ to the path to your boundary conditions files that you have generated from a global simulation. I suspect that you are trying to run for a simulation date where you have no boundary conditions.

[Naaimaben]

Hi @yantosca, thank your for your response.
I have indeed changed the path on my HEMCO_Config.rc file

#==============================================================================
# --- GEOS-Chem boundary condition file ---
#==============================================================================
(((GC_BCs
* BC_  /home/xx/gc_025x03125_geosfp_fullchem/OutputDir/GEOSChem.BoundaryConditions.$YYYY$MM$DD_$HH$MNz.nc4 SpeciesBC_?ADV? 1900-2100/1-12/1-31/* EFY xyz 1 * - 1 1
)))GC_BCs

[yantosca]

@Naaimaben Is it possible that you boundary conditions for your simulation are missing? Could you also please upload the log file from your simulation to this issue?

[Naaimaben]

GC.log

I did download the boundary condition file from the harvard input data website to /Output folder.

[yantosca]

Thanks for the update @Naaimaben. The boundary conditions on the Harvard data site are only intended for testing and development. They do not contain a full day of data. You need to create your own boundary conditions by running a global simulation to archive the BoundaryConditions collection diagnostic first before running the nested simulation.

I would also refer you to our documentation of the nested-grid simulation workflow on our ReadTheDocs site.

[Naaimaben]

Really sorry for the confusion @yantosca, yes I am indeed running a global simulation and get the error in the log file.

[yantosca]

Thanks for the log file @Naaimaben I see this output:

 Processing container: BC_AONITA
 Parsing source file and replacing tokens
 Reading from existing stream: /home/naaima.benkadour/gc_025x03125_geosfp_fullchem/OutputDir/GEOSChem.BoundaryConditions.20190701_0000z.nc4
HEMCO: Entering GET_TIMEIDX (HCOIO_UTIL_MOD.F90) ( 6)
 Number of time slices found:            8
 Time slice range :    201907010000.00000        201907012100.00000
          preferred datetime:  201907010000.
 Data is 3-hourly. Entire day will be read.
              selected tidx1:              1
    corresponding datetime 1:  201907010000.
              selected tidx2:              8
    corresponding datetime 2:  201907012100.
        assigned delta t [h]:              3
 local time?  F
HEMCO: Leaving GET_TIMEIDX (HCOIO_UTIL_MOD.F90) ( 6)
 
HEMCO ERROR: Cannot find field BC_AONITA. Please check variable name in the config. file

I think this means that there isn't a boundary condition variable in the file for the AONITA species. AONITA was introduced in 14.5.0 with a bunch of new chemistry/emissions updates. This could mean that your boundary conditions file is from a pre-14.5.0 simulation. Regenerating the boundary conditions with the same version of the model you are using should fix this error.